ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.8161+8G>A

gnomAD frequency: 0.00559  dbSNP: rs199569003
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV003891878 SCV000305789 benign PKD1-related condition 2019-08-29 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001000002 SCV000604718 benign Polycystic kidney disease, adult type 2020-01-29 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001000002 SCV002797762 likely benign Polycystic kidney disease, adult type 2021-07-21 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003221886 SCV003917457 likely benign not provided 2023-09-01 criteria provided, single submitter clinical testing PKD1: BP4, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001353764 SCV000592817 benign Autosomal dominant polycystic kidney disease no assertion criteria provided clinical testing The PKD1 c.8161+8G>A variant was identified in 3 of 550 proband chromosomes (frequency: 0.005) from individuals or families with ADPKD (Rossetti 2002, Rossetti 2012). The variant was also identified in dbSNP (ID: rs199569003) as “NA”. In 1000 Genomes Project the variant is identified in 13 of 5000 chromosomes (frequency: 0.0026); in NHLBI GO Exome Sequencing Project in 46 of 7726 European American (frequency: 0.006) and in 4 of 3742 African American alleles (frequency: 0.001). The variant was identified in the Exome Aggregation Consortium database (March 2016) in 133 (4 homozygous) of 18570 chromosomes (freq. 0.007) in the following populations: Finnish in 5 of 120 chromosomes (freq. 0.04), other in 4 of 168 chromosomes (freq. 0.02), European (Non-Finnish) in 74 of 7230 chromosomes (freq. 0.01), Latino in 6 of 660 chromosomes (freq. 0.009), African in 6 of 1220 chromosomes (freq. 0.005) and South Asian in 38 of 8060 chromosomes (freq. 0.005), but was not seen in the East Asian population, increasing the likelihood this could be a low frequency benign variant. The variant is also identified in GeneInsight COGR (classified as benign) and in ADPKD database 4x as likely neutral. The c.8161+8G>A variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. In silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.

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